web
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TmMolStar


			
				
					
						
						
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			<h1>@rcsb/rcsb-saguaro-3d</h1>
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				<a href="#rcsb-saguaro-3d" id="rcsb-saguaro-3d" style="color: inherit; text-decoration: none;">
					<h1>rcsb-saguaro-3D</h1>
				</a>
				<p>RCSB Saguaro Web 3D is an open-source library built on the top of the <a href="https://rcsb.github.io/rcsb-saguaro">RCSB Saguaro 1D Feature Viewer</a>
					and <a href="https://github.com/rcsb/rcsb-molstar">RCSB Molstar</a> designed to display protein features at the <a href="https://www.rcsb.org">RCSB Web Site</a>.
					The package collects protein annotations from the <a href="https://1d-coordinates.rcsb.org">1D Coordinate Server</a>
					and the main <a href="https://data.rcsb.org">RCSB Data API</a> and generates Protein Feature Summaries.
				The package allows access to RCSB Saguaro and Molstar methods to add or change the displayed data. </p>
<div id="pfv"></div>
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        trackHeight: 20,
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        displayColor: "#f17070",
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        trackData: [{
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            end: 50
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];
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    boardConfig: {
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            max: 245
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        disableMenu:true,
        rowTitleWidth: 80,
        trackWidth: 670,
        includeAxis: true
    },
    rowConfig: rowConfigChainA,
    sequenceSelectionChangeCallback: function (plugin, selectorManager, sequenceRegion) {
        selectorManager.clearSelection("select", { modelId: "1acb_board", labelAsymId: "A" });
        plugin.clearSelection("select", { modelId: "1acb_board", labelAsymId: "A" });
        if (sequenceRegion.length > 0) {
            var regions = sequenceRegion.map(function (r) {
                var _a;
                return ({
                    modelId: "1acb_board",
                    labelAsymId: "A",
                    region: { begin: r.begin, end: (_a = r.end) !== null && _a !== void 0 ? _a : r.begin, source: "sequence" }
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                var _a;
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                    modelId: "1acb_board",
                    labelAsymId: "A",
                    begin: e.begin,
                    end: (_a = e.end) !== null && _a !== void 0 ? _a : e.begin
                });
            }), "hover", "set");
    },
    structureSelectionCallback: function (plugin, pfv, selection) {
        var sel = selection.getSelectionWithCondition("1acb_board", "A", "select");
        if (sel == null) {
            pfv.clearSelection("select");
            plugin.resetCamera();
        }
        else {
            pfv.setSelection({ elements: sel.regions, mode: "select" });
        }
    },
    structureHoverCallback: function (plugin, pfv, selection) {
        var sel = selection.getSelectionWithCondition("1acb_board", "A", "hover");
        if (sel == null)
            pfv.clearSelection("hover");
        else
            pfv.setSelection({ elements: sel.regions, mode: "hover" });
    }
};
var fvConfigChainB = {
    boardId: "1acb.B_board",
    boardConfig: {
        range: {
            min: 1,
            max: 70
        },
        disableMenu:true,
        rowTitleWidth: 80,
        trackWidth: 670,
        includeAxis: true
    },
    rowConfig: rowConfigChainB,
    sequenceSelectionChangeCallback: function (plugin, selectorManager, sequenceRegion) {
        selectorManager.clearSelection("select", { modelId: "1acb_board", labelAsymId: "B" });
        plugin.clearSelection("select", { modelId: "1acb_board", labelAsymId: "B" });
        if (sequenceRegion.length > 0) {
            var regions = sequenceRegion.map(function (r) {
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                    modelId: "1acb_board",
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            plugin.resetCamera();
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        var _a;
        if (d != null)
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    },
    sequenceHoverCallback: function (plugin, selectorManager, elements) {
        if (elements == null || elements.length == 0)
            plugin.clearSelection("hover");
        else
            plugin.select(elements.map(function (e) {
                var _a;
                return ({
                    modelId: "1acb_board",
                    labelAsymId: "B",
                    begin: e.begin,
                    end: (_a = e.end) !== null && _a !== void 0 ? _a : e.begin
                });
            }), "hover", "set");
    },
    structureSelectionCallback: function (plugin, pfv, selection) {
        var sel = selection.getSelectionWithCondition("1acb_board", "B", "select");
        if (sel == null) {
            pfv.clearSelection("select");
            plugin.resetCamera();
        }
        else {
            pfv.setSelection({ elements: sel.regions, mode: "select" });
        }
    },
    structureHoverCallback: function (plugin, pfv, selection) {
        var sel = selection.getSelectionWithCondition("1acb_board", "B", "hover");
        if (sel == null)
            pfv.clearSelection("hover");
        else
            pfv.setSelection({ elements: sel.regions, mode: "hover" });
    }
};
var blockChainA = {
    blockId: "chainA",
    featureViewConfig: [fvConfigChainA]
};
var blockChainB = {
    blockId: "chainB",
    featureViewConfig: [fvConfigChainB]
};
var blockSelectorElement = function (blockSelectorManager) {
    return (React.createElement("div", null,
        React.createElement("select", { onChange: function (e) {
                    blockSelectorManager.setActiveBlock(e.target.value);
                } },
            React.createElement("option", { value: "chainA" }, "Chain A"),
            React.createElement("option", { value: "chainB" }, "Chain B"))));
};
var customConfig = {
    blockConfig: [blockChainA, blockChainB],
    blockSelectorElement: blockSelectorElement
};
var sequenceConfig = {
    title: undefined,
    subtitle: undefined,
    config: customConfig
};
var molstarConfig = {
    loadConfig: {
        loadMethod: "loadPdbIds",
        loadParams: [{
            pdbId: "1acb",
            id: "1acb_board"
        }]
    },
    pluginConfig: {
        showImportControls: true,
        showSessionControls: false
    },
};
document.addEventListener("DOMContentLoaded", function (event) {
    var panel3d = new RcsbFv3D.custom({
        elementId: "pfv",
        structurePanelConfig: molstarConfig,
        sequencePanelConfig: sequenceConfig,
        cssConfig: {
            overwriteCss:true,
            rootPanel:{
                display:"flex",
                flexDirection:"column-reverse"
            },
            structurePanel:{
                width: 750,
                height: 700
            },
            sequencePanel:{
                width:750,
                marginBottom:5
            }
        },
    });
    panel3d.render();
});
</script>
				<a href="#cdn-javascript" id="cdn-javascript" style="color: inherit; text-decoration: none;">
					<h3>CDN JavaScript</h3>
				</a>
				<p><code>&lt;script src=&quot;https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-3d@1.0.0/build/dist/app.js&quot; type=&quot;text/javascript&quot;&gt;&lt;/script&gt;</code></p>
				<a href="#node-module-instalation" id="node-module-instalation" style="color: inherit; text-decoration: none;">
					<h3>Node Module Instalation</h3>
				</a>
				<p><code>npm install @rcsb/rcsb-saguaro-3d</code></p>
				<a href="#building-amp-running" id="building-amp-running" style="color: inherit; text-decoration: none;">
					<h2>Building &amp; Running</h2>
				</a>
				<a href="#build-app" id="build-app" style="color: inherit; text-decoration: none;">
					<h3>Build app</h3>
				</a>
				<pre><code><span class="hljs-built_in">npm</span> install
<span class="hljs-built_in">npm</span> run buildApp</code></pre>
				<a href="#build-examples" id="build-examples" style="color: inherit; text-decoration: none;">
					<h3>Build examples</h3>
				</a>
				<pre><code>npm <span class="hljs-builtin-name">run</span> buildExamples</code></pre><p>From the root of the project:</p>
				<pre><code>http-server -p PORT-<span class="hljs-built_in">NUMBER</span></code></pre><p>and navigate to <code>localhost:PORT-NUMBER/build/examples/</code></p>
				<a href="#main-classes-and-methods" id="main-classes-and-methods" style="color: inherit; text-decoration: none;">
					<h3>Main Classes and Methods</h3>
				</a>
				<a href="#assembly-view" id="assembly-view" style="color: inherit; text-decoration: none;">
					<h4>Assembly view</h4>
				</a>
				<p>Class <strong><code>RcsbFv3DAssembly</code></strong> (<code>src/RcsbFv3D/RcsbFv3DAssembly.tsx</code>) builds a predefined view for PDB entries. This method is used in the RCSB PDB web portal
					to display 1D features on PDB entries (ex: <a href="https://www.rcsb.org/3d-sequence/4HHB">4hhb</a>). Its configuration requires a single PDB ID.
				In addition, <code>RcsbFvAdditionalConfig</code> allows to configure the feature viewer as describe in <a href="%22https://rcsb.github.io/rcsb-saguaro-app/index.html%22">rcsb-saguaro-app API</a></p>
				<pre><code class="language-typescript"><span class="hljs-keyword">interface</span> RcsbFv3DAssemblyInterface <span class="hljs-keyword">extends</span> RcsbFv3DAbstractInterface {
   <span class="hljs-attr">config</span>: {
        <span class="hljs-attr">entryId</span>: <span class="hljs-built_in">string</span>;
        title?: <span class="hljs-built_in">string</span>;
        subtitle?: <span class="hljs-built_in">string</span>;
    };
    additionalConfig?: RcsbFvAdditionalConfig;
}</code></pre>
				<p>Source code example can be found in <code>src/examples/assembly/index.ts</code>.</p>
				<a href="#custom-view" id="custom-view" style="color: inherit; text-decoration: none;">
					<h4>Custom view</h4>
				</a>
				<p>Class <strong><code>RcsbFv3DCustom</code></strong> file <code>src/RcsbFv3D/RcsbFv3DCustom.tsx</code> builds a customized view between one or more feature viewers and a single Molstar plugin.
				The configuration interface encodes the parameters needed for the feature viewers (<code>sequencePanelConfig</code>) and the molstar plugin (<code>structurePanelConfig</code>).</p>
				<pre><code class="language-typescript"><span class="hljs-keyword">interface</span> RcsbFv3DCustomInterface <span class="hljs-keyword">extends</span> RcsbFv3DAbstractInterface {
    <span class="hljs-attr">structurePanelConfig</span>: RcsbFvStructureInterface;
    sequencePanelConfig: {
        <span class="hljs-attr">config</span>: CustomViewInterface;
        title?: <span class="hljs-built_in">string</span>;
        subtitle?: <span class="hljs-built_in">string</span>;
    };
}</code></pre>
				<p><img src="https://raw.githubusercontent.com/rcsb/rcsb-saguaro-3d/master/.github/img/config_img.png" alt="Alt text" title="Custom config schema"></p>
				<p>Information in the sequence panels is organized in blocks where each block contains the parameter
					(<code>blockConfig</code>) to display one or more feature viewers. The optional parameter <code>blockSelectorElement</code> defines a React component
					that renders the html element used to change the displayed block. The class <code>BlockSelectorManager</code> is used to select which block is
					displayed. For example, <code>blockSelectorManager.setActiveBlock(&quot;myBlock&quot;)</code> will display the feature viewers defined in the block
					with <code>blockId</code> <code>&quot;myBlock&quot;</code> (see <code>FeatureBlockInterface</code>). Additionally, <code>blockChangeCallback</code> defines a function that will be executed
				when the displayed block changes.</p>
				<pre><code class="language-typescript"><span class="hljs-keyword">interface</span> CustomViewInterface {
    <span class="hljs-attr">blockConfig</span>: FeatureBlockInterface | <span class="hljs-built_in">Array</span>&lt;FeatureBlockInterface&gt;;
    blockSelectorElement?: <span class="hljs-function">(<span class="hljs-params">blockSelector: BlockSelectorManager</span>) =&gt;</span> JSX.Element;
    blockChangeCallback?: <span class="hljs-function">(<span class="hljs-params">plugin: SaguaroPluginPublicInterface, pfvList: <span class="hljs-built_in">Array</span>&lt;RcsbFv&gt;, selection: RcsbFvSelectorManager</span>) =&gt;</span> <span class="hljs-built_in">void</span>;
}</code></pre>
				<p>Source code example can be found in <code>src/examples/multiple-chain/index.ts</code>.</p>
				<p>Each block must contain a unique block identifier (<code>blockId</code>) and the configuration for all the feature viewers that will be rendered
				when the block is activated (<code>featureViewConfig</code>).</p>
				<pre><code class="language-typescript"><span class="hljs-keyword">interface</span> FeatureBlockInterface {
    <span class="hljs-attr">blockId</span>:<span class="hljs-built_in">string</span>;
    featureViewConfig: <span class="hljs-built_in">Array</span>&lt;FeatureViewInterface&gt; | FeatureViewInterface;
}</code></pre>
				<p>The interface fo each feature viewer defines its dynamic interaction with the molstar plugin through different event callbacks</p>
				<ul>
					<li><code>sequenceSelectionChangeCallback</code> defines how the molstar plugin reacts when the feature viewer selection changes</li>
					<li><code>sequenceElementClickCallback</code> defines how the molstar plugin reacts when a feature viewer element (positional annotation) is clicked</li>
					<li><code>sequenceHoverCallback</code> defines how the molstar plugin reacts when the mouse hovers the feature viewer or any element</li>
					<li><code>structureSelectionCallback</code> defines how the protein feature viewer reacts when the molstar plugin selection changes</li>
					<li><code>structureHoverCallback</code> defines how the protein feature viewer reacts when displayed models on the molstar plugin are hovered</li>
				</ul>
				<pre><code class="language-typescript"><span class="hljs-keyword">export</span> <span class="hljs-keyword">interface</span> FeatureViewInterface {
    boardId?:<span class="hljs-built_in">string</span>;
    boardConfig: RcsbFvBoardConfigInterface;
    rowConfig: <span class="hljs-built_in">Array</span>&lt;RcsbFvRowConfigInterface&gt;;
    sequenceSelectionChangeCallback: <span class="hljs-function">(<span class="hljs-params">plugin: SaguaroPluginPublicInterface, selectorManager: RcsbFvSelectorManager, sequenceRegion: <span class="hljs-built_in">Array</span>&lt;RcsbFvTrackDataElementInterface&gt;</span>) =&gt;</span> <span class="hljs-built_in">void</span>;
    sequenceElementClickCallback: <span class="hljs-function">(<span class="hljs-params">plugin: SaguaroPluginPublicInterface, selectorManager: RcsbFvSelectorManager, d: RcsbFvTrackDataElementInterface</span>) =&gt;</span> <span class="hljs-built_in">void</span>;
    sequenceHoverCallback: <span class="hljs-function">(<span class="hljs-params">plugin: SaguaroPluginPublicInterface, selectorManager: RcsbFvSelectorManager, hoverRegion: <span class="hljs-built_in">Array</span>&lt;RcsbFvTrackDataElementInterface&gt;</span>) =&gt;</span> <span class="hljs-built_in">void</span>;
    structureSelectionCallback: <span class="hljs-function">(<span class="hljs-params">plugin: SaguaroPluginPublicInterface, pfv: RcsbFv, selection: RcsbFvSelectorManager</span>) =&gt;</span> <span class="hljs-built_in">void</span>;
    structureHoverCallback: <span class="hljs-function">(<span class="hljs-params">plugin: SaguaroPluginPublicInterface, pfv: RcsbFv, selection: RcsbFvSelectorManager</span>) =&gt;</span> <span class="hljs-built_in">void</span>;
}</code></pre>
				<a href="#contributing" id="contributing" style="color: inherit; text-decoration: none;">
					<h2>Contributing</h2>
				</a>
				<p>All contributions are welcome. Please, make a pull request or open an issue.</p>
				<a href="#license" id="license" style="color: inherit; text-decoration: none;">
					<h2>License</h2>
				</a>
				<p>The MIT License</p>
				<pre><code><span class="hljs-attribute">Copyright</span> (c) <span class="hljs-number">2021</span> - now, RCSB PDB and contributors</code></pre><p>Permission is hereby granted, free of charge, to any person obtaining a copy
					of this software and associated documentation files (the &quot;Software&quot;), to deal
					in the Software without restriction, including without limitation the rights
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